Dunno about the boot switch but regarding the "always on stereo". You need to get this bit right when fitting a new stereo.
On that multi-pin plug on the back of the stereo there is usually two power pins - one connected directly to the battery to provide proper power and another that switches on with the ignition key, a sort of "power sense" connection. Most stereos are in a sort of sleep mode when you switch them off and they still draw current. They are only truly "off" when they detect no volts at the pin that connects to the ignition key.
Things work different on the alfa (as always). On my car (at least) the main power pin and the "power detect" pin were wired together with a jump lead. There is only a connection to the battery and no connection to the ignition switch. This means you can install a new stereo without any modifications and everything seems to work. The problem is that your new stereo will be drawing a little current when switched off AND when the engine is switched off. If you leave your car unused for just a couple of days or so you'll discover a flat battery!
You have to snip that little jumper lead in the multi-pin plug that connects to your stereo and then connect a lead from the plug to a power point that is fed via the ignition switch (hardly any current is drawn from this so you shouldn't overload anything). I found one that had been previously installed with a nokia hands-free kit.
Its worth checking you've got things right by checking the current draw from your car battery when the car isn't "switched on", just in case.
(sorry if this post reads badly, I'm in a rush!)